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Figure 1: Transcriptional analysis of the CXCL4-induced M4 macrophage

(A) The upper graph shows log2 transformed intensity of all expressed genes in M0 macrophages plotted against the intensity in M4 macrophages (r=0.934, P<0.0001). The lower plot shows the same data including only genes with a FDR<0.05 as determined by Local Pooled Error (LPE) test. (B) Heatmap showing all significantly differentially regulated genes (FDR<0.05 by LPE test). Gene expression was normalized and standardized (Gene list in Supplementary table S1). Red indicates high, green low gene expression. Genes and conditions were allowed to freely cluster in the y and x axis, respectively. (C) Modified Principal Components Analysis of M1 and M2 gene expression data (as described in Methods). Briefly, M4 gene expression data were plotted into a coordinate space defined by M1 and M2 gene expression data. (D) Hierarchical clustering of the normalized M1, M2, and M4 gene expression data. All genes were included in the analysis, and the results are displayed as dendrogram. Root = M0. #1, #2, and #3 indicate donor-specific replicates for each condition.